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    <p>On my end if I build your project using the <code>pom.xml</code> you've showed us, with <code>apache-poi</code> declared after <code>jfreechart</code>, then as you've mentioned I get a corrupt JAR. Swapping the order of these two dependencies indeed gives me a correct JAR.</p> <p>I've some previous experience with the <code>maven-shade-plugin</code> and when I used it I had trouble with the created JAR's <code>META-INF</code> directory, so I've checked that for defects.</p> <p>I've tried to copy (using Total Commander) the <code>META-INF</code> directory somewhere on my local filesystem and what I've noticed is that there were errors while copying the files in <code>META-INF/licences/</code>. If I've tried to copy those somewhere individually and it worked but I couldn't copy the whole thing. My conclusion was that the JAR/ZIP archive is corrupt.</p> <p>What I did was I <em>entered</em> that JAR in Total Commander (<kbd>Ctrl</kbd>+<kbd>PgDown</kbd> <em>over</em> the JAR file) and I <em>renamed</em> <code>thirdpartylicenses.txt</code> to <code>thirdpartylicenses.txt.wtf</code>. Doing this Total Commander offers to save this and it repackages the JAR (I've the Total7zip Total Commander packer plugin installed - if anyone tries this and it doesn't work try it with this installed).</p> <p>After this. It works.</p> <p>(I've also tried to repack the whole thing without renaming anything using Cygwin's <code>unzip</code>/<code>zip</code> commands, but that didn't work the new archive was still corrupt. Total Commander or the plugin I've mentioned does some magic.)</p> <p>I guess the <code>maven-shade-plugin</code> merely creates a corrupt or invalid ZIP/JAR archive. I'm not sure why and maybe what I've described won't work for anyone else but I thought I'd mention it so maybe I could help.</p> <hr> <p>I couldn't just leave this alone, so I've dug deeper and I think I've found the answer.</p> <p>The <em>bad</em> JAR contains 65608 entries. The <em>good</em> JAR contains 65450 entries.</p> <p>Guess what's the upper limit of <a href="http://en.wikipedia.org/wiki/ZIP_%28file_format%29#ZIP64" rel="nofollow noreferrer">the number of entries for a <em>plain</em> ZIP file</a>? Yeah. The Wiki article speaks about a ZIP64 format which overcomes this limitation.</p> <p>The <em>good</em> JAR has less entries because the actual dependencies change because of the position of the dependency declarations in your <code>pom.xml</code>. (<a href="https://stackoverflow.com/a/13088093/433835">As described by this answer.</a>)</p> <p>I've counted the entries like this.</p> <pre><code>Collections.list(new JarFile("...").entries()).size(); </code></pre> <p>I was using <a href="https://stackoverflow.com/a/9616474/433835">Java 7 which seems to support the new ZIP64 format</a>, so maybe if someone tries to count the entries in the <em>bad</em> JAR using Java 5 or 6 will receive an error (I'm not sure though).</p> <p>I also tried to run the JAR <em>exploded</em>. I've unpacked the whole JAR into a directory and run the whole thing like this.</p> <pre><code>java -cp &lt;dir/ com.mycompany.test.Start </code></pre> <p>Worked like a charm.</p> <hr> <p>Bottom line. Don't <em>overuse</em> the <code>maven-shade-plugin</code>.</p> <p>I have a project at work where I build my project like this.</p> <ul> <li>I copy my project's dependencies using the <a href="http://maven.apache.org/plugins/maven-dependency-plugin/" rel="nofollow noreferrer"><code>maven-dependency-plugin</code></a>. Checkout the <a href="http://maven.apache.org/plugins/maven-dependency-plugin/copy-dependencies-mojo.html" rel="nofollow noreferrer"><code>copy-dependencies</code> goal</a>. This copies your dependencies into <code>target/dependency</code> if I remember correctly.</li> <li><p>Using the <a href="http://maven.apache.org/plugins/maven-jar-plugin/" rel="nofollow noreferrer"><code>maven-jar-plugin</code></a> I add these dependencies to my final JAR's <code>MANIFEST.MF</code> as <code>Class-Path</code> entries using these options in the plugins configuration.</p> <pre><code>&lt;classpathPrefix&gt;dependency/&lt;/classpathPrefix&gt; &lt;addClasspath&gt;true&lt;/addClasspath&gt; </code></pre> <p>So I'll have <code>Class-Path</code> entries like <code>dependency/&lt;artifactId&gt;-&lt;version&gt;.jar</code>, etc.</p></li> <li>After this I'm using the <a href="https://maven.apache.org/plugins/maven-assembly-plugin7" rel="nofollow noreferrer"><code>maven-assembly-plugin</code></a> to create a distribution ZIP which contains my final JAR and the whole <code>dependency/</code> folder.</li> <li>When I deploy my application I can run it like <code>java -jar final.jar</code>.</li> </ul> <p>Primarily I've opted to use this solution, because in my project I use some Bouncy Castle JARs which JARs have some extravagant <em>this and that</em> inside their <code>META-INF</code> directory. When I used the <code>maven-shade-plugin</code> to create my final runnable JAR all hell broke loose and I got nasty <em>that method couldn't be found and this signature is not quite right</em> errors.</p> <p>You should be doing something like this also. This Maven shade business is too <em>shady</em> to be useful (pun intended).</p> <hr> <p>Here's <a href="http://ath3nd.wordpress.com/2013/12/25/packaging-a-multimodule-maven-spring-app-in-a-standalone-jar/" rel="nofollow noreferrer">a blog post on the whole process that I've tried to describe</a> just above (thanks to <a href="https://stackoverflow.com/users/487649/baba">baba</a>), maybe it'll help someone in the future.</p>
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    1. COThat's a really good job you've done there! I agree that this is the problem. +1;
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    2. COWow, thanks for the comment. I need to have a look tomorrow.
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    3. COA work-around: In java 7, it works with 'java -cp final.jar MainClass' but not 'java -jar final.jar' when the number of entries is over 2^16.
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